Just one thing, I forgot to add chomp in the 5th line of my code...

#!/usr/bin/perl -w
use strict;

print "Please enter the file name\n";
my $in = <STDIN>;
chomp($in);
open inFile, '<', $in;
open outFile, '>', 'out.txt';

while (<inFile>) {
    my $line = $_;
    # ... do stuff to $line here
    print outFile $line;
}

close inFile;
close outFile;
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